LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.9946083 3.9946083 3.9946083 Created orthogonal box = (0.0000000 -62.907155 0.0000000) to (38.522608 62.907155 9.7847522) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2133238 6.0877892 6.5231681 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -62.907155 0.0000000) to (38.522608 62.907155 9.7847522) create_atoms CPU = 0.003 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2133238 6.0877892 6.5231681 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -62.907155 0.0000000) to (38.522608 62.907155 9.7847522) create_atoms CPU = 0.003 seconds 1491 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 11 34 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2976 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_623376124862_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.433 | 6.433 | 6.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9639.5568 0 -9639.5568 6996.2723 72 0 -9758.6931 0 -9758.6931 465.33451 Loop time of 4.32846 on 1 procs for 72 steps with 2976 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9639.55676974536 -9758.68413123429 -9758.69313004843 Force two-norm initial, final = 93.270197 0.20816212 Force max component initial, final = 22.284237 0.026581551 Final line search alpha, max atom move = 1.0000000 0.026581551 Iterations, force evaluations = 72 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2449 | 4.2449 | 4.2449 | 0.0 | 98.07 Neigh | 0.049417 | 0.049417 | 0.049417 | 0.0 | 1.14 Comm | 0.013283 | 0.013283 | 0.013283 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02089 | | | 0.48 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8735.00 ave 8735 max 8735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391180.0 ave 391180 max 391180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391180 Ave neighs/atom = 131.44489 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.055 | 6.055 | 6.055 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -9758.6931 0 -9758.6931 465.33451 47423.713 74 0 -9758.7196 0 -9758.7196 21.580823 47477.135 Loop time of 0.137193 on 1 procs for 2 steps with 2976 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9758.69313004843 -9758.71519587257 -9758.71959783452 Force two-norm initial, final = 35.069013 1.6090595 Force max component initial, final = 33.886285 1.2967533 Final line search alpha, max atom move = 0.00010570414 0.00013707220 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1351 | 0.1351 | 0.1351 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003142 | 0.0003142 | 0.0003142 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001784 | | | 1.30 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9059.00 ave 9059 max 9059 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391378.0 ave 391378 max 391378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391378 Ave neighs/atom = 131.51142 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.193 | 6.193 | 6.193 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9758.7196 0 -9758.7196 21.580823 Loop time of 2.091e-06 on 1 procs for 0 steps with 2976 atoms 191.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.091e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9042.00 ave 9042 max 9042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391276.0 ave 391276 max 391276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391276 Ave neighs/atom = 131.47715 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.193 | 6.193 | 6.193 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -9758.7196 -9758.7196 38.582098 125.8204 9.7801972 21.580823 21.580823 30.037845 -9.0355992 43.740224 2.5479878 1146.6839 Loop time of 2.692e-06 on 1 procs for 0 steps with 2976 atoms 334.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.692e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9042.00 ave 9042 max 9042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195638.0 ave 195638 max 195638 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391276.0 ave 391276 max 391276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391276 Ave neighs/atom = 131.47715 Neighbor list builds = 0 Dangerous builds = 0 2976 -9758.71959783452 eV 2.54798776514362 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05